The Wilpons are going to have to do some hard thinking about the realities of this team, and decide whether Omar, Willie, or the players are mostly to blame. IMO, unless you are talking about a situation where you have a team with just one bad player or bad apple (e.g., Nomar, Bonilla, etc.), then it has to fall on the GM or manager. Either the GM assembled a team with overrated talent, declining talent, or poor attitudes, or the manager has failed to properly utilize and motivate that talent. When an entire team underperforms, I have to look squarely at management.
So for the Mets, which is it? Is it mostly on Omar or Willie? Not entirely clear-cut, IMO. Take Omar first. He has certainly made some very impressive moves as GM, including the trades for Santana and Church. I'll even throw bringing Pedro over here in there, since he was solid in '06. On the negative side, however, Omar has shown a propensity to pursue declining talent on the downside of their careers (Delgado, Green, Valentin, Castillo, Alou, El Duque, ...) Furthermore, I found his unwillingness to re-sign Bradford and Oliver as two of the most bone-headed moves of all time. Both of those players continue to perform very well to this day, and quite likely would have been the difference between a collapse in '07 and playoffs.
In addition, I think it's important to keep in mind that Omar hasn't exactly had the toughest job in the world: he has essentially been given the largest budget of any NL team over the past 4 years. It's not like he's been asked to assemble a WS-class team with the budget of the Rays or Marlins. Omar also apparently doesn't seem to understand the need for a few vocal leaders in the clubhouse, since he has assembled a team of veterans who do not want to lead.
On the other hand, I think you can easily make a case that despite all the injuries, there is no reason this team should not be in 1st place in NL East. The core of the team - Reyes, Wright, and Beltran - have all remained healthy. The collapse at the end of '07 was inexcusable, due in large part IMO to Willie's overuse of bullpen during regular season. I also think Willie needs to take a more pro-active stance in developing Reyes, whose talent is still very raw. I think Willie's unwillingness to show emotion during a game and argue with umps is also a problem. I especially don't like the way he manages the bullpen, pulls starters early, and juggles the lineup.
At the end of the day, I'm not sure whether more of the blame lies with Willie or Omar, but I can say that the present team is not responding well to Willie. I can also say that even if Wilpon replaces Willie, he ought to put Omar on notice that his job is also on the hot seat, and he needs to re-consider the type of players the team really needs going forward.